UC Davis Bioinformatics Training Program

Bioinformatics courses, boot camps and workshops presented by the University of California, Davis Bioinformatics Core

Bioinformatics Training from the University of California

Next generation DNA sequencing technology is touted as enabling the next wave of the genomics revolution.  Massively-parallel generation of DNA “reads” makes it possible to sequence entire genomes the size of the human genome, within days and for a few thousands dollars.  It also allows individual laboratories to do research that was previously only possible at large genome centers. The widespread availability of this technology is stimulating the development of a large array of innovative approaches to genome-wide investigations, but comes at the cost of sparse or incomplete training opportunities for these advancing technologies. We at the University of California, Davis Bioinformatics Core seek to change that by offering a number of varied length workshops focusing on various aspects of bioinformatics and biostatistics.

We offer a number of intensive workshops on RNA-seq, data analysis and visualization, and cloud computing with a focus on leveraging Amazon’s computing resources.  During our week-long workshops, we cover in-depth the practical theory and application of cutting-edge next-generation sequencing techniques. We also host a number of intensive but easy-to-digest 1-day events providing practical answers and hands-on techniques to the hottest topics in bioinformatics. All training events provide ample time for personalized help from workshop professors.

Our bioinformatics workshops are perfectly suited to your learning curve through this personalized attention whether you are a scientist, academic instructor, industry professional, or graduate student.

For more information on training offerings, you may check back here periodically, or contact us directly with any questions.


Announcing our newest Amazon Machine Image

We are pleased to announce the release of our newest Galaxy/command-line Amazon Machine Image. The new features of this AMI include updated versions of all of the bioinformatics software, updated and fixed Galaxy tool interfaces, and a Galaxy FTP server that makes it easy to transfer large files to Galaxy. Instructions on how to launch this new AMI and how to use the Galaxy FTP server are located on our software page. We hope that all of your research endeavours are going well and we hope to hear from you or see you in a workshop sometime soon!

2014 Bioinformatics Training Schedule Announced

The Bioinformatics Core is pleased to announce three training opportunities which will be held at UC Davis in 2014:

Please click on the links to get full information about each opportunity. We hope to see you this year!

Next Generation Sequencing Library Preparation Workshop, October 28 – 29, 2013

October 28 – 29, 2013, our friends at the DNA Technologies Core will be hosting a great workshop for you wetlab enthusiasts out there.  The text from the workshop announcement is below, or you can view the original PDF.

Next Generation Sequencing (NGS) has revolutionized the way that we address complex biological questions. As sequencing output rapidly increases and experimental scales get bigger, library preparation becomes one of the major bottlenecks for NGS. This course provides a comprehensive hands-on training on how to prepare high quality libraries for Illumina HiSeq2500 and MiSeq sequencing platforms. Participants are encouraged to bring their own total RNA template and, by the end of the course, will have a library ready for NGS sequencing. Lectures will cover the entire workflow including sample QC/QA, as well as the basic principles of NGS technology and consideration for experimental design meeting current publication standards. The course will highlight applications such as mRNA-seq, ChIP-seq, de novo sequencing, re-sequencing, mutation discovery, single cell genomics, and PacBio RSII. A case example of combinatorial usage of NGS technology to meet specific biological goals of sequencing will be explored.

Protocols covered in this course are compatible with multiplexing as well as with the preparation of PCR-free, ribosomal RNA depleted, and strand specific libraries. As sequencing capacities continually increase, automation of library construction is becoming indispensible. We will demonstrate the automation systems IntegenX Apollo 324 (small – medium throughput)and Caliper Sciclone NGS G3 (medium – high throughput). The workshop will maintain a highly interactive environment to maximize communication among attendees as well as with lab instructors. The workshop will conclude with an evaluation of libraries and a discussion session focusing on each participant’s experimental design to help maximize efficiency and output of sequencing experiments.

Course materials and lunches will be provided. To apply contact: Dr. Ryan Kim, rwkim@ucdavis.edu